Dataset contains the daily averaged results of calculations of turbulent fluxes of CO2 based on measurements in an apple orchard located in Bądków (51.7 N, 20.8 E), about 60 km south of Warsaw. The results include data on net CO2 exchange (NEE) as well as components related to absorption (GPP) and emission (Reco) of this gas. Additionally it includes data of basic meteorological parameters: total shortwave radiation [Rg] and air temperature [Ta], being the main dynamic factors determining CO2 exchange variability. The collection includes two sets of data for the time series: 8.08.2024 – 10.08.2024 and 16.05.2025 – 07.02.2026.